CDKN1C p.186AP[3]
c.567_608del · rs2133782940 · VCV1141211
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000327%, nfe)
Conditions
2
Beckwith-Wiedemann syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -1.2 |
| Region caveats | ||
| Repeat context | tandem | G-rich low complexity, simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000327%
European (non-Finnish) · 3/917,892 alleles
Filtering AF
8.7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.4e-05%
Overall
0.000305%
3/982,762 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CDKN1C
- Protein
- p.186AP[3]
- Coding
- c.567_608del
- MANE Select
- NM_001122630
- dbSNP
- rs2133782940
- Type
- Deletion
- Location
- chr11:2884849 (GRCh38)
- Gene constraint
- LOEUF 1.943 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.93
Similar variants
- CDKN1C p.Pro137fs Pathogenic ★★ same condition
- CDKN1C p.Ser73fs Pathogenic/Likely pathogenic ★★ same condition
- CDKN1C p.Val130fs Pathogenic/Likely pathogenic ★★ same condition
- CDKN1C p.Ala246_Ala252del Uncertain significance ★★ same condition
- CDKN1C p.Gly242_Ala245del Uncertain significance ★★ same condition
- CDKN1C c.787+16_787+25del Likely benign ★★ same condition
- CDKN1C p.168_169AP[5] Likely benign ★★ same condition
- CDKN1C p.186_187AP[5] Likely benign ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdkn1c-p-186ap-3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown